About Rationally Speaking

Rationally Speaking is a blog maintained by Prof. Massimo Pigliucci, a philosopher at the City University of New York. The blog reflects the Enlightenment figure Marquis de Condorcet's idea of what a public intellectual (yes, we know, that's such a bad word) ought to be: someone who devotes himself to "the tracking down of prejudices in the hiding places where priests, the schools, the government, and all long-established institutions had gathered and protected them." You're welcome. Please notice that the contents of this blog can be reprinted under the standard Creative Commons license.

Tuesday, September 11, 2012

Jerry Coyne vs John Dupré on the status of evolutionary theory

by Massimo Pigliucci

I read two interesting commentaries on evolutionary theory recently. One was by philosopher John Dupré, the other by evolutionary biologist Jerry Coyne. Actually, the latter was a commentary on the former, and it had a typical Coyne-style title (“Another philosopher proclaims a nonexistent ‘crisis’ in evolutionary biology”). I know both Jerry and John, and I respect them as scholars in their respective fields. As a biology-philosopher crossover myself, I also appreciate (no matter how often I may disagree on the specifics, particularly with Jerry) their respective forays into each other’s field. It is this kind of interdisciplinary cross-talk that makes the life of the intellect particularly exciting for me, and which has the potential to generate further understanding, both within academia and the public at large.

In this case, I have to say that both Jerry and John are (partially) wrong, though for different reasons. Perhaps an analysis of these reasons will shed some light on the actual current status of evolutionary theory, as well as on the always treacherous relationship between philosophy and science.

Jerry begins his commentary with the usual fiery words I have come to expect from him: “We often see molecular biologists (e.g., James Shapiro) and philosophers (e.g., Thomas Nagel and Jerry Fodor) proclaiming the imminent death of modern evolutionary theory, so someone who wears both hats could be especially muddled — and dangerously misleading. And my suspicions were correct.” I have been critical of Fodor myself, and I dread seeing Nagel’s forthcoming book for similar reasons. Moreover, I do share Jerry’s rejection of Shapiro’s ideas about evolution. But John has always struck me as a reasonable fellow with interesting things to say, so I was a bit weary of Jerry’s quick dismissal of his piece.

As it turns out, Jerry had a point in chastising John: contra the latter, there is no “crisis” in evolutionary theory. However, most of Dupré’s essay is much more nuanced than it would appear from Jerry’s selective quotations, and it is nowhere near the nonsense that Jerry Fodor and Massimo Piattelli-Palmarini have recently written about evolution.

Indeed, much of John’s commentary uses rather mild language. While Dupré does mention Thomas Khun’s concept of paradigm change in science, he explicitly says that the new developments in evolutionary biology do not constitute a revolution, but rather a “major, progressive reorganization of existing knowledge, without undermining the fundamental tenets of evolutionary theory.” Dupré ends the article by stating that “Evolutionary theory’s current contretemps — and our inability to predict where the field will be in 50 years — are a cause for celebration,” because they show that science changes through better understanding and new empirical discoveries, a dynamism that he explicitly contrasts with the fossilized attitudes of creationists and intelligent design proponents.

Seen from Coyne’s perspective, though, Dupré’s essays goes too far and needs to be taken to task. Jerry states that “What bothers me is that, like so many others, [Dupré] casts these new discoveries as things that throw the theory of evolution in crisis. And that plays into the hands of creationists, no matter how strongly Dupré decries creationism.” Ironically, John had foreseen such a move, and had written in his own essay: “Radically rethinking evolutionary theory invariably attracts the attention of creationists, who gleefully announce that if professional advocates of Darwinism cannot agree, the concept must be in retreat. And, evolutionists, confronted with this response, tend to circle the wagons and insist that everyone is in agreement.” The only thing I find objectionable about that excerpt is that the appropriate word is “significantly,” not “radically.”

So what is going on here? Setting aside John’s a bit overhyped talk of crisis, as well as Jerry’s unnecessarily sharp defense of the purity of evolutionary theory, where is the meat of the disagreement? Dupré lists a number of new discoveries and accompanying conceptual advances that — he claims — are bringing about a rethinking of the Modern Synthesis (often incorrectly labelled “neo-Darwinism”) of the 1930s and ‘40s, which constitutes the equivalent of the Standard Model in evolutionary biology. These include:

* The rejection of the idea that life’s evolution is best represented as a branching tree, because horizontal gene transfer, especially early on, and particularly among prokaryotes (not to mention frequent speciation by hybridization in plants), is better visualized as yielding a network of genetic relatedness among organisms.

* The discovery that mutation is not the only generator of heritable variation (to be precise, a second one, recombination, had always been in play as well), again because of exchanges of chunks of genomes between organisms, and occasionally even of full genomes, as in the case of the origin of eukaryotic cells by symbiosis of different types if bacteria.

* The discovery of a complex layer of epigenetic effects that mediate between genes, environment and development in a way that opens up the possibility of causal loops in which genes produce epigenetic factors (such as methylation patterns, iRNAs, etc.), which in turn respond to environmental stressors by altering the expression of other genes. Note that some of these epigenetic effects act across generations, and some show stability over evolutionarily significant lengths of time (as documented here, here and here).

Nonsense, responds Coyne, deploying two well worn strategies of conservative scientists (I don’t mean the term politically here, of course): minimization and absorption of novelty. For instance:

“Yes, we’ve known for a while that microbes can have ‘wide gene exchange‘ — movement of chunks of DNA between distantly related species of bacteria. ... This hasn’t really changed the theory of evolution one iota, though it’s changed our view of where organisms can acquire new genes.” (Well, it depends on what Jerry means by “the theory of evolution,” and on just how much change would count — in his view — for more than “one iota.”)

[Concerning the role of horizontal gene transfer and symbiosis] “This is true, but what Dupré doesn’t mention — and I hope he knows better, because he should if he’s learned anything about evolution — is that these big events of symbiosis that produced mitochondria, chloroplasts, and perhaps flagella, are extremely rare, and we’ve known that for a few decades.” (Besides the unnecessarily patronizing tone toward Dupré, is Coyne saying that rare events are unimportant? It is likely because of the very long term effects of a rare event — an asteroid impact — that a primate rather than a dinosaur is writing this blog, and “extremely rare” endosymbiosis has created cells with nuclei, which have made multicellularity possible, which in turn has changed the course of evolution in countless and dramatic ways. Jerry here is confusing infrequent with unimportant. Imagine a physicist telling his readers that the Big Bang wasn’t a crucial part of physics’ view of the cosmos, because after all it only happened once!)

“Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.” (This is incorrect, as we do have examples of long term heritability of epigenetic changes — see links above — and besides, I thought evolution took place generation by generation, which means that any heritable change, no matter how short lived, has the potential to alter the evolutionary trajectory of a population, however indirectly.)

And of course Jerry just has to include a veiled ad hominem in his attack on Dupré: “Dupré doesn’t seem to be a goddie, but he still seems susceptible to the nebulous woo of ‘top down causation.’” No, Dupré isn’t a “goddie,” whatever that may be, and his causal talk is perfectly understandable: all he means is that the arrows of causality in evolution, genetics and development go in all sorts of directions, not just from the genes upward: genes produce proteins which help building cells, but environmental signals often cause genes to be transcribed or silenced, development is the result of epigenetically mediated interactions between genes and environments, and of course — as Jerry himself states, natural selection is the mother of top down causal processes in biology.

As it turns out, Dupré has — I think — not gone far enough, leaving out a number of other crucial points that would have strengthened his case and undermined Coyne’s response. The decades since the Modern Synthesis (MS) have seen also the rise to prominence in evolutionary biology of phenotypic plasticity, a ubiquitous phenomenon that helps understand how gene-environment interactions affect population dynamics and that was dismissed as noise by early supporters of the MS. Moreover, contra the received wisdom, multi-level selection (including group and even species selection or sorting) are here to stay, greatly enriching the theoretical arsenal of evolutionary biologists beyond the one provided by the MS (which, of course, in turn had greatly enhanced the original Darwinism, which had indeed undergone an actual crisis at the turn of the 20th century). Want more? How about the now well documented phenomenon of “facilitated variation,” which shows how natural selection has apparently to do much less work than previously thought, because a good number of biological structures develop by taking advantage of the physico-chemical properties of cells rather than by direct genetic encoding of countless details? Or the fact that paleontologists have now convincingly shown that macroevolutionary dynamics are not simply reducible to the sort of microevolutionary ones that are the only conceptual arsenal of the MS? Or perhaps Jerry should consider the fantastic empirical and theoretical work on evolvability, robustness and modularity, ideas that are entirely alien to the MS?

Jerry concludes his critique of John’s essay thusly: “As an evolutionary biologist — which Dupré is not — I think I’d know if my field was in crisis.” No Jerry, plenty of us have been telling you that a change is in the cards (though, again, not a crisis!), you just haven’t been listening.

Very good! My only complaint is that you say at the beginning that it isn't really a crisis, and then in the last sentence you say it is... I would have mentioned more issues, such as developmental plasticity and multi-level selection, but I was only allowed 900 words.

It's fascinating how the various methods of producing phenotypic variations is so similar to a good creative process in the arts(philosophically). Unit level randomized change, various methods of recombination at component levels(with different sources for the recombination fodder).

The feedback loop of epigenetic effects is interesting as well. Such plasticity holds an obvious advantage over rigidity.

The only crisis is if you hold too tightly to your former conception of what evolution should entail. I could see worldviews becoming entrenched after a lifetime swimming through the details.

Epigenesis is the interesting one on the list for me. Broadly speaking, we don't know the potential of chemicals to bond in different ways in the cellular condiditons existing at mutation. To say mutations are entirely random without a complete view of bonding potential, and that there are no Epigenetic affects, is too bold. I like Epigenesis because it is consistent with the fundamental idea in my free book at www.thehumandesign.net that the organism is the embodiment of the environmental chemicals used for its construction.

The organism is a biological arrangement of chemicals encoded by DNA, with all else coming from outside the Zygote for it to grow & divide. DNA can only use the chemical capacities in its immediate proximity to build cells. Mediation by RNA and perhaps other factors would be important in that embodiment, by sensitizing the DNA mutations to the environment in which they arise, rather than being entirely "random" (chemicals will bond or not by their potentials, and not "randomly" anyway, so the extent of the non-randomness is the issue).

This fits in nicely with a further important idea in my book, that the pre-existing environmental chemical capacities and their proximities & arrangements may predetermine what can be constructed. I have found that few biologists state clearly that Selection is post mutation and function, and weakly or non-predictive as to what might change in function by mutation until it has arisen. A pre-existing environment and embodiment of it (greatly assisted by Epigenesis but perhaps not requiring it if mutations are prolific enough) would predetermine what functions might be constructed in the first place to then be selected. A must read free book, with lots of information filling in details.

> “Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.” (This is incorrect, as we do have examples of long term heritability of epigenetic changes — see links above — and besides, I thought evolution took place generation by generation, which means that any heritable change, no matter how short lived, has the potential to alter the evolutionary trajectory of a population, however indirectly.) <

"Epigenetics" seems like it might lend some support to a form of Lamarckism. (I would think that would be a fairly significant change.)

> No, Dupré isn’t a “goddie,” whatever that may be, <

I would suspect that "goddie," in this context, means one who believes in theistic evolution - theistic in the sense that evolution is divinely guided (or at least, divinely influenced). (For example, evolutionary biologist Ken Miller would qualify as a "goddie.")

> Jerry concludes his critique of John’s essay thusly: “As an evolutionary biologist — which Dupré is not — I think I’d know if my field was in crisis.” No Jerry, plenty of us have been telling you, you just haven’t been listening. <

You seem to be equivocating. Which one is it? Is the field of evolutionary biology in crisis or not?

To the last question: no it isn't. It'd be if the phenomena that Massimo describes accounts for more cases of adaptive evolution than regular gradual natural selection.

Now, Massimo says that Coyne is wrong for dismissing things like endosymbiosis for being rare, even if those rare ocurrences led to very significant evolutionary innovations. Well, Coyne isn't saying those things didn't happen; I think he means that the rarity of their occurrence precludes us from making much predictions, models, frameworks, etc... revolving around them.

What's more, you could argue that endosymbiosis is an extreme case of coevolutionary symbiosis, something that's not really beyond the scope of current evolutionary theory.

epigenetic inheritance as understood in the 21st century has nothing to do with Lamarckism.

> Which one is it? Is the field of evolutionary biology in crisis or not? <

I made it explicitly clear in the post that I don't think the field is in crisis. The last sentence, directed to Coyne, is about the fact that plenty of professionals have been telling Coyne that his dismissal of the new developments as anything more than icing on the cake is unwarranted.

Under "Epigenetics" Wiki mentions a possible connection to Lamarck: "if a mutation in the DNA has been caused in sperm or egg cell that results in fertilization, then some epigenetic changes are inherited from one generation to the next. This raises the question of whether or not epigenetic changes in an organism can alter the basic structure of its DNA, a form of Lamarckism."

Temporary adjustments without changes to DNA would be interesting, but the encoding of the changes in DNA itself rather than its expression would be more radical. The temporary form would be part of the way to Lamarckism, and the permanent form would be near enough (although to what extent is also unknown). Perhaps mutations under the Central Dogma are prolific enough to create the environmentally diverse organisms we know about. Or, perhaps those evolutions have been assisted by environmental factors pressing upon the organism to favor suitable mutations. I shall wait & see.

that's the problem with Wikipedia, when it comes to pretty technical issues. If you read some of the resources linked in the main post you'll get a good appreciation of why epigenetic inheritance has nothing to do with Lamarckism.

Yes, Wiki mentions, its a start, not a concluded view. Do you have some papers to advance the argument or do you just wait for others to provide them artikat? Wiki only mentions "possible connections" and "raises the question". These are open issues due to the complexity of chemical bonding in general and cellular conditions at mutation. While some experts might leave them as such until greater certainty, others might wish to immediately close off the possibility. I shall wait & see and read more, particularly if artikat can contribute some useful references rather than obvious one-line tips.

I'm really not sure how it's a theory in crisis when the contention is largely an extension (or refinement) of the core ideas rather than overthrowing the accepted wisdom. Even by Kuhnian standards, it seems sensationalist.

I wonder how so many diverse functional sequences of DNA, even if recombined within & between closely related species, can have mutated from random nucleotide errors in replications passed on by the germ line. A human still looks to me a bit like a 747 assembled by a whirlwind, even if step by step in successful sequences over billions of years, but maybe clear statistical analyses of its likelihood exist somewhere (a hell of a job if its been done).

> epigenetic inheritance as understood in the 21st century has nothing to do with Lamarckism. <

That's not what my sources are telling me.

"Interest in Lamarckism has recently increased, as several studies in the field of epigenetics have highlighted the possible inheritance of behavioral traits acquired by the previous generation." (emphasis mine)

"if a mutation in the DNA has been caused in [a] sperm or egg cell that results in fertilization, then some epigenetic changes are inherited from one generation to the next.[12] This raises the question of whether or not epigenetic changes in an organism can alter the basic structure of its DNA (see Evolution, below), a form of Lamarckism." (emphasis mine)

> I made it explicitly clear in the post that I don't think the field is in crisis. The last sentence, directed to Coyne, is about the fact that plenty of professionals have been telling Coyne that his dismissal of the new developments as anything more than icing on the cake is unwarranted. <

Well, you may have explicitly stated one thing in one place; but you implicitly stated another thing in another place. And I'm not the only one who noticed this (as was made evident by John Dupre's post).

The bottom line is this: Coyne holds that the mechanism of random variation and natural selection working in tandem is the "SOLE process producing adaptation (the appearance of design)" (his words, not mine). So, if this is not the primary mechanism for evolutionary adaptation (which, no doubt, the general public has been lead to believe that it is), then that would seem to me to constitute a major change in evolutionary thinking.

Seriously? You go with Wikipedia over what a professional who actually works in the field tells you? How postmodern of you.

> Well, you may have explicitly stated one thing in one place; but you implicitly stated another thing in another place. <

In my book explicit trumps implicit, especially after one is asked to clarify and one responds in no uncertain terms. But that doesn't fit your agenda, does it?

> if this is not the primary mechanism for evolutionary adaptation (which, no doubt, the general public has been lead to believe that it is), then that would seem to me to constitute a major change in evolutionary thinking. <

Nope. Few people - if any - argue that adaptations can arise by anything other than natural selection. The debate is about the theoretical import of many other mechanisms in evolution, and note that even Darwin knew that selection wasn't the only thing at play.

Professionals differ in opinions, and I will have a go at some papers eventually (added to my long reading list). To date, I have been most interested in neuroscience papers, given that we did evolve with mental abilities by mutation (with or without feedback from the environment) and that is a very open field. Nevertheless I will keep open the "possibilities" & "questions" about Lamarckism until then, given the unknowns about how the elements of the Periodic Table combine as compounds to become humans and complex organisms generally.

"There have been rumblings for some time to the effect that the neo-Darwinian synthesis of the early twentieth century is incomplete and due for a major revision.... Evolution in Four Dimensions is the most recent addition to this genre, and contributes yet another valuable perspective to the discussion." Massimo Pigliucci Nature"

> In my book explicit trumps implicit, especially after one is asked to clarify and one responds in no uncertain terms. But that doesn't fit your agenda, does it? <

I have you on record saying that the neo-Darwinian synthesis is "incomplete and due for a MAJOR revision" (your words, not mine). (You stated in your above blog that "the only thing I find objectionable about [Dupre's] excerpt is that the appropriate word is “significantly,” not “radically.”)

> Nope. Few people - if any - argue that adaptations can arise by anything other than natural selection. <

Even Coyne himself admitted (in his video lecture) that this is "subject to dispute."

"And finally...the last part of evolutionary theory and in many ways the very important one ... is what causes evolution...and I will maintain that the vast amount of evolutionary change, ALTHOUGH THIS IS SUBJECT TO DISPUTE, is the result of the process of natural selection..."

Lamarckism is not inconsistent with Darwin's selection (the prevailing view of selection). It is just different from the other mechanisms of inheritance (if it can be inherited) and it shortcuts the randomness if the usual mechanisms in the Epigenetic individual (possibly willfully) if it not hereditable. Selection operates on anything thrown up to it, whether by the more random means of standard mechanisms or epigenetically, but epigenetics is different for the above reasons. The entity is slected by the environment at all times during its existence, and the mechanisms survive with it.

It seems to me that if the environment has altered gene expression to the extent that the alteration is passed down, any mutations will have that cellular context. It might increase the likelihood that mutations tend that way rather than being entirely random if Weissman's barrier is not strict.

However, alternatively, importantly, IF such mutations arise, the organism would be ready to immediately make use of them in regular functions it has already build around environmental factors, aiding the survival of mutations in the new form - a bit of seamlessness in transition rather than the odd new type just popping anew into the environment to struggle with survival.

If the new expressions are consistent with new mutations across a population rather than one or a few individuals, it would benefit survival of the eventual mutations if they follow in a population. I see it as a possible, wide, transition that eases any isolation and random jerkiness of mutation under Weissman, quite apart from whether the new expressions directly lead to new mutations that suit them.

To clarify my lazy third para, the idea is that temporary epigentic change might prime a population or group within a population for permanent mutation to individual(s) to catch on in seamless integration and breeding for the spread of the permanent change.

I hope Coyne & Dupre get to read this, because the difficulty I have with professionals is that they don't make rational extrapolations from established facts to explain and to point the way to the new discoveries. This is quite apart from whether mutations will be prompted by the epigenetic cells. As above, temporary Epigenesis might prepare a polulation for a mutation to catch on if it follows that epigentic pattern, for the indiviuals to be immediately functional and accepted in a population for breeding.

Anther example, mentioned in other threads here, are the fact that an organism can be seen as a literal embodiment of the environmental chemicals used for its constructions, so look to the properties of a particular chemical environment to see what, in the first place, can be constructed, even before that vairation is selected.

A third example is the reluctance to admit that Selection is expost the variation and construction of the entity with that variation to be selected. Consequently on a harsh view it is non-scientific as it is expost and not predictive. However, my second example points the way to how prediction might apply, by looking at the chemical environment used by DNA to construct cells.

Professionals need to be valued, but rationality, incisiveness, and so on, are far more valuable in my view, no matter the source of the analysis. Science needs to open up to the public to source those with an ability for rationality over and above anything else.

The most recent DNA change to the human genome I have read about happened in New Guinea about 9,000 years ago, a small one, so it's hard to imagine it happening at all, let alone by Epigenetics. In a more general setting of evolution, consider whether Epigenetics might prepare a population for the acceptance of actual DNA changes IF those changes arise in individuals (randomly or otherwise) for breeding within the population.

> Is it possible that human culture can have any effect in the DNA sequence of the individuals? <

No, that would truly represent Lamarckism. What has been documented, however, is that environmental changes can affect the degree of methylation of DNA sequences (that's an epigenetic effect), which in turn can modulate the expression of certain genes.

Alastair,

> Do you consider Eva Jablonka a professional? <

Yes, if you bothered to check the links in the post you would have discovered that she is one of the suggested readings. Yes, I know she likes to use the word "Lamarckian," but not only is she a tiny minority in the field, she is actually using it in a very technical, historically accurate sense that doesn't really reflect what we are talking about here. She is one of the few people I know who actually read Lamarck...

> I have you on record saying that the neo-Darwinian synthesis is "incomplete and due for a MAJOR revision" <

Yup, since when a major revision is the same as a crisis? Forgot to check your Wiki dictionary this time?

> Even Coyne himself admitted (in his video lecture) that this is "subject to dispute." <

You are not paying attention. Jerry there is talking about evolutionary change, which is much broader than adaptation.

> Yeah, Darwin himself subscribed to some element of Lamarckism. <

You really ought to take up some more serious reading than Wikipedia. Yes, it is well known that Darwin flirted with Lamarckism for a while, because he didn't have a theory of inheritance (Mendel was working on one, but Darwin didn't know it). He quickly dropped Lamarckism, though, as well as his own theory of blended inheritance.

Alastair, "the vast amount of evolutionary change, ALTHOUGH THIS IS SUBJECT TO DISPUTE, is the result of the process of natural selection..." You correctly identify a contradiction by Coyne (maybe a small one), as evolutionary change is change by adaptation. There is no other means of evolutionary change, so Massimo avoids your point on the grounds of some unstated distinction or other that is hard to imagine. And continue to use Wiki, it's a great reference for catching out Massimo. Persevere with it through his objections - check them out for accuracy, relevance, context & subjectivity.

> There is no other means of evolutionary change, so Massimo avoids your point on the grounds of some unstated distinction or other that is hard to imagine. <

You may want to consider writing less and reading more. Particularly, reading about population genetics. There are at least four other standard evolutionary mechanisms other than natural selection recognized by all practicing biologists: mutation, recombination, drift and migration. A good primer can be found here:

Massimo, I won't bother considering that until I run out of ideas. How can I not write when there is so much nonsense to respond to? All those factors serve adaptation of the organism to the environment - change by natural selection. Coyne is not raising whether selection is preceded by inheritence, obviously it is. He is raising whether selection is displaced by Epigenetics as Lamarckism, if Epigenetic change is also inherited.

Selection is the only means of evolutionary change, and it is after inheritence to test what is inherited. However, it is eroded if the organism has "selected itself" by Epigenetic change becoming inherited. Your reference to "mutation, recombination, drift and migration" is to the existing regime for inheritence that is selected. The omission of "epigenetics" shows you have missed the point - that it would not be selected ex post inheritence if the organism changes by its own activities in the environment.

I am starting to wonder if you realize that selection is everything in current evolutionary theory, which is why Coyne & others are touchy. Your mechanisms of inheritence are also selected, believe it or not. If the environment did not support the living product of those mechanisms by selecting them for survival, those mechanisms would not exist. I just don't understand why you sling me advice when you are in no position to do so in this argument or any with me that I can recall offhand, yet you persist. That's stubborn, but not wise.

Considering this and the recent threads about Smolin & Ladyman, I am beginning to wonder if diversionary advice & tactics are your main weapon in preference to reasoning. That can happen in every walk of life, when backs are to the wall, but I hope you can rise above it.

as much as I have enjoyed the not-so-playiful back and forth, I have limited patience for being insulted on my own blog. Consider this a friendly warning: stick to substance or your next comment will not be posted.

Speaking of substance:

> Selection is the only means of evolutionary change <

This is flat out wrong, as an even cursory examination of any population genetics or evolutionary biology textbook will readily show. The other four mechanisms I mentioned above are routinely recognized as complementary to natural selection. The latter is the only mechanism widely recognized to generate *adaptation*, but adaptive evolution is a subset of evolutionary broadly construed.

> The omission of "epigenetics" shows you have missed the point - that it would not be selected ex post inheritence if the organism changes by its own activities in the environment. <

It shows nothing of the sort. I brought up epigenetics in the main post, but the list I gave you above was explicitly presented as the one universally accepted by biologists to contribute to evolutionary change. Epigenetics is getting there, but it is *not* universally recognized.

> Yes, I know she likes to use the word "Lamarckian," but not only is she a tiny minority in the field, she is actually using it in a very technical, historically accurate sense that doesn't really reflect what we are talking about here. <

If Jablonka is actually using the term "Lamarckism" in a "very technical" and "historically accurate sense," then her definition of the term really does reflect what we are talking about here. Or, at least, it really does reflect what I am talking about here - namely, that epigenetics seems to smack of Lamarckism.

Jerry Coyne: "Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.” (emphasis mine)

Your response to that comment (as stated in your blog essay above): "This is incorrect, as we do have examples of long term heritability of epigenetic changes ." (emphasis mine)

If we have evidence that epigenetic changes are long term, then we have evidence for some form of Lamarckism. (It should be noted that I have already cited a reliable source (your objections to Wikipedia notwithstanding) that this is the basis of the dispute concerning epigenetics.)

> Yup, since when a major revision is the same as a crisis? Forgot to check your Wiki dictionary this time? <

I see...mea culpa. I must apologize for not fulling appreciating the nuances involved here. You believe it is appropriate to characterize evolutionary theory as requiring a MAJORrethinking. However, you believe it is inappropriate to characterize evolutionary theory as requiring a RADICALrethinking.

It should be noted that Eva Jablonka and Marion Lamb both consider the changes in evolution to be "revolutionary." It should also be noted that you endorsed their "MINORITY" opinion. (I have already cited evidence to support this claim.)

"Ideas about heredity and evolution are undergoing a REVOLUTIONARY change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes" (emphasis mine)

You initiate the back & forth on each & every occasion, so don't blame me for bringing it into focus & the context of our discussions. It seems to have worked, and we might now have some sensible discussion. If you stay on track, there is no reason for me to deviate. As I said above: "Your mechanisms of inheritence are also selected, believe it or not. If the environment did not support the living product of those mechanisms by selecting them for survival, those mechanisms would not exist."

Selection is a much broader concept than you appear to realize. Selection acts upon whatever DNA throws up as a phenotype by whatever mechanism, as long as it is not Epigenetic. In acting upon that phenotype, it acts upon the mechanism. Selection determines adaptation (by definition an adaptation to the enviroment, not an adaptation to the mechanisms). The mechanism is selected along with the organism.

It doesn't matter to me whether you or any other biologist would say the organism adapts to the mechanisms of inheritence, or prefers the normal use of the term for adaptation to the environment. It adapts by necessary use of one mechanism or another, as I have explained, but the mechanisms are selected along with the organism. The umbrella of selection is absolute. The point is what survives.

"Your mechanisms of inheritence are also selected, believe it or not. If the environment did not support the living product of those mechanisms by selecting them for survival, those mechanisms would not exist."

I can't really believe you think Massimo doesn't know this. I am sure he has forgotten more population biology than you will ever know.

Your statement is of course true, but I think you are confusing absolute with relative fitness. All you need is to be "fitter" than the others in your local population. A mutation could confer lower fitness and still become fixed, if "fitter" members die (storm, freeze, habitat destruction). Mutations can even be neutral. This is all classical population genetics - mutation, migration, drift and selection balance.

I appreciate the reference to absolute & relative fitness, but I'm not sure it adds anything to whether Selection is the driver of Adaptation (the original issue). Fitness is absolute in an environment. An environment includes other entities, including ones' own species or population. Consequently, relative fitness is a subset of absolute, which is environmental selection at the end of the day. The issue Coyne was raising is that broad, to deal with what is outside that absolute process of Selection (Epigenetics) rather than what is within it as relative fitness as a subset. That's all. It's a definitional storm in a teacup to me, which is why I bought in to the argument.

I should say, "outside the absolute process of Selection (Epigenetics) as currently understood", with Epigenetics adding willfulness, for example, rather than simple (or complex) random mutation and sorting.

I should ask how "sure" you are Michael, "that Massimo has forgotten more population genetics than I will ever know". Didn't you read Massimo and my exchange on manners immediately preceding your comment? Is that a substantive argument or by use of a Ouija Board to determine what I will ever know and what Massimo has forgotten.

Have I made my point without spelling it out further? In case I haven't, your post is irrelevant to the substantive point (as explained by me above) and your Ouija Board reading is an irrelevancy build upon that irrelevancy. That is an awful standard of reasoning, necessitating this additional "I should (respond to the additional complete nonsense)" post.

> Or, at least, it really does reflect what I am talking about here - namely, that epigenetics seems to smack of Lamarckism. <

The key word there is "seems." Yes, superficially, but Jablonska's take on Lamarckism is not the sort of Wikipedia-style inheritance of acquired characteristics you keep using.

> If we have evidence that epigenetic changes are long term, then we have evidence for some form of Lamarckism. <

No, because the environment is not encoding anything adaptive that gets transmitted to the next generation. What happens is that some environmental stressors alter the pattern of, say, methylation. This may or may not be adaptive, which means that natural selection still needs to mediate the effects, which means we are not talking Lamarckism.

> I must apologize for not fulling appreciating the nuances involved here. <

Well, you do seem to have a problem with nuance. There is a difference between a major expansion of evolutionary theory (my view) and a crisis. I don't know how else to explain it, the English ought to be clear enough.

> It should also be noted that you endorsed their "MINORITY" opinion. <

See? there goes your problem with nuances again. All you have shown is that I gave a positive review to their book, which I stand buy. That is a far cry from endorsing everything they say, in or outside the book.

> Much of evolutionary change was caused by natural selection, which is the SOLE process producing ADAPTATION <

Once again, there is very little debate about what causes adaptation: it is selection. The debate is on the first part of Coyne's contention: how much *other* (i.e., non-adaptive) evolutionary change is caused by what mechanism. But even Coyne - as a population geneticist - recognizes the importance of the four additional mechanisms I mentioned above.

Marcus,

> As I said above: Your mechanisms of inheritence are also selected, believe it or not. <

Of course I believe it, where did I say I don't? But you keep confusing types of mechanisms. For instance, mutation is not a mechanism of inheritance, it is a mechanism of variation. Yes, mutations may (or may not) be selected, or they may evolve in a population by drift.

> Selection is a much broader concept than you appear to realize. Selection acts upon whatever DNA throws up as a phenotype by whatever mechanism, as long as it is not Epigenetic. <

I think you are not conceiving of selection broadly enough. There is nothing that precludes selection from acting on epigenetic inheritance.

> It doesn't matter to me whether you or any other biologist would say the organism adapts to the mechanisms of inheritence <

Not only I have never said any such thing, but the sentence is meaningless as it stands. Organisms do not adapt (populations do), and mechanisms of inheritance are adaptations, they cannot be adapted to.

Then firstly, getting back to whether Selection is the sole means of Adaptation (Coyne's issue), you would agree it is, because your mechanisms of inheritence are also selected. This is a semantic storm in a tea cup because relative fitness (Michael Fugate's summary above) is a subset of absolute fitness to the environment.

You may have misunderstood the connection I was making to Epigenetics. Selection will act on Epigenetic change after the entity has, in an extreme example, willed their own changes by changed habits. That's the crucial difference, rather than whether it must then survive in its environment (which it obviously must do). It means that to some extent an adaptation is fashioned by the living entity, rather than thrown up by the mechanism (including mutation) before it lives.

Mutations are of less concern than relative competition in populations, which is where the argument headed, but they are inherited nonetheless. They are a mechanism for variation in inheritence. This is another factor under hereditability (or its limits, including random variation). These are definitional storms in teacups, which is why I got involved in the first place. Mechanisms for inheritence include variation in inheritence by random mutation, by definition.

> No, because the environment is not encoding anything adaptive that gets transmitted to the next generation. What happens is that some environmental stressors alter the pattern of, say, methylation. This may or may not be adaptive, which means that natural selection still needs to mediate the effects, which means we are not talking Lamarckism. <

That qualifies as Lamarckian (according to Jablonka and Lamb).

"These [methylation patterns in DNA and chromatin marks] are considered "Lamarckian" in the sense that they are responsive to environmental stimuli and can differentially affect gene expression adaptively, with phenotypic results that can persist for many generations in certain organisms."

Jablonka and Lamb are not challenging "natural selection" per se, but the idea that "all variations in the hereditary material are random" and that "all hereditary variations are variations in DNA base sequences." (source: pg. iv, "Epigenetic Inheritance and Evolution: The Lamarckian Dimension" by Eva Jablonka and Marion Lamb)

> Well, you do seem to have a problem with nuance. There is a difference between a major expansion of evolutionary theory (my view) and a crisis. I don't know how else to explain it, the English ought to be clear enough. <

I really don't see a significant difference between a "MAJOR" expansion (your view) and a "RADICAL" expansion (Dupre's view).

> See? there goes your problem with nuances again. All you have shown is that I gave a positive review to their book, which I stand buy. That is a far cry from endorsing everything they say, in or outside the book. <

I see. So, what exactly are you endorsing or not endorsing?

> Once again, there is very little debate about what causes adaptation: it is selection. The debate is on the first part of Coyne's contention: how much *other* (i.e., non-adaptive) evolutionary change is caused by what mechanism. But even Coyne - as a population geneticist - recognizes the importance of the four additional mechanisms I mentioned above.

"mechanisms of inheritance are adaptations, they cannot be adapted to" Wrong, and that would be the nub of your misunderstanding. Mechanisms of inheritence are nothing until the environment has determined that they are adaptations. They are not adaptations. They are a mechanism throwing up something for the environment to decide. Unless the mechanism is Epigenetic and enables the organism to throw something up while alive to undercut the unknowns of the standard mechanisms, the mechanism is in limbo until the actual entity is selected for survival.

To say mechanisms of inheritence are adaptations is to put the cart before the horse, and, more specifically, it assumes that the mechanism produces adaptations. As above, they only make presentations for the environment to determine adaptations, and they are not predetermining what an adaptation may be. There is no predetermination under any current mechanism of inheritence (save perhaps for Shapiro in an extreme view of his work beyond its actual reach). Problem solved for you, no charge.

On the final point of Massimo's just above, I'm not okay with 'Okay. Fair enough' Alastair, unless non-adapative means Epigenetic (which is a different kind of adaptation - not needing to wait till something is thrown up, because the entity is making it happen in life) and the four additional mechanisms are NOT seen as adaptiions (my argument directly above). The other mechanisms are an organized lottery for the environment to approve expost.

> Jablonka's and Lamb's peer-reviewed article is entitled "Evidence, mechanisms and models for the inheritance of acquired characteristics". <

It doesn't change the fact that their view is a minority one and that most people have concluded that they are wrong at calling epigenetic inheritance Lamarckism.

> That qualifies as Lamarckian (according to Jablonka and Lamb). <

Yes, and they are wrong.

> Jablonka and Lamb are not challenging "natural selection" per se, but the idea that "all variations in the hereditary material are random" and that "all hereditary variations are variations in DNA base sequences." <

They are correct in the second challenge, wrong in the first one.

> I really don't see a significant difference between a "MAJOR" expansion (your view) and a "RADICAL" expansion (Dupre's view). <

Well, first of all there is a difference of emphasis. But what I (and Coyne) object to is the use of the word "crisis."

> So, what exactly are you endorsing or not endorsing? <

I said it several times, including just above: epigenetic inheritance is real, but there is no ground to call it Lamarckian.

Marcus,

> Mechanisms of inheritence are nothing until the environment has determined that they are adaptations. <

That is not entirely correct (there are such things as neutral phenotypic traits), and at any rate it is true for any established phenotype that has undergone selection. We were talking about the current status of inheritance mechanisms, not their origin.

> Unless the mechanism is Epigenetic and enables the organism to throw something up while alive to undercut the unknowns of the standard mechanisms <

That doesn't make sense to me. Epigenetic mechanisms are also subject to environmental selection.

> To say mechanisms of inheritence are adaptations is to put the cart before the horse, and, more specifically, it assumes that the mechanism produces adaptations. <

Nowhere does that conclusion follows from anything I said.

> There is no predetermination under any current mechanism of inheritence <

Nor has anyone suggested that.

> Problem solved for you, no charge. <

There was no problem to solve, so no charge would be justified...

> unless non-adapative means Epigenetic (which is a different kind of adaptation - not needing to wait till something is thrown up, because the entity is making it happen in life) <

That sentence contains a contradiction: either epigenetic mechanisms are adaptive or their are not, they can't be both.

> the four additional mechanisms are NOT seen as adaptiions (my argument directly above). The other mechanisms are an organized lottery for the environment to approve expost. <

Incorrect, for instance cultural transmission is likely an adaptation, and by the way is the only one of the proposed mechanisms that truly does behave in a Lamarckian fashion.

Saying inheritance mechanisms are adaptations makes the assumption that they will survive to become adaptations. In themselves they are just sorting mechanisms. Their current status is original at all times. The idea of there being an orgin to them is meaningless. They either exist to present something to the environment in every new individual or they do not. They are an ongoing open presentation for selection of adaptations, and not simply "adaptations" as you propose. The rest of my argument logically follows from that.

Epigenetics are subject to selection. They are adaptations. They are different in kind from adaptations under the other mechanisms. They occur while living, not by merely being thrown up in a sorting mechanism. Quite simple to understand. Education or culture might be a temporary form of Epigenetics, and not inherited as far as I am aware, but perhaps you can enlighten. If they are not inherited, strike them from relevancy to this argument. I assume there is no evidence they are inherited, and are therefore irrelevant.

I'm confused about all this. I think you are on to something when you say this is about semantics, so lets define the terms.

First lets take an example of an inheritance mechanism, so we know what kind of things we are talking about here.

In a diploid genome a gene sometimes have two alleles, one major (X) and one minor (x). The three combinations XX, Xx and xX all gives rise to the same trait and the combination xx gives rise to a different trait.

Now is this what you are referring to when you talk about inheritance mechanisms? Can you please give some more examples.

When reading your different responses you sometimes say that this kind of mechanism is:

- Selected ("Your mechanisms of inheritence are also selected", September 13, 2012 11:00 AM)- Never selected ("Mechanisms of inheritence are nothing until the environment has determined that they are adaptations. They are not adaptations.", September 14, 2012 7:27 AM and "They are an ongoing open presentation for selection of adaptations, and not simply "adaptations" as you propose.", September 14, 2012 9:18 AM)

So which one is it?

Do you mean "mechanisms of inheritance" when you say only "mechanisms" or do they refer to different things.

What do you mean by "Mechanisms of inheritence are nothing until..."? Sureley they are something (at least 'inheritence mechanisms').

Read my last two posts, or the full thread of discussion, as I am not going to summarize it for you here. Specifically, to show your reasoning error in the 'Selected' and 'Never Selected' example, the mecahnisms are selected by the environment as adaptations along with the entity itself if it survives. They are not 'Never Selected', they are selected as adaptations along with the entity at all times, every second of its life, and consequently they are in themselves just a presentation for selection by the environment at all times and not simply "adaptations". The environment is the only cause of adaptation, which is the issue here.

Educate yourself with examples of the mechanisms, which are explained by Massimo throughout, and in the article (absent Epigenetics, which is a different kind of mechanism). In any event the principles stated in these posts apply to ALL mecahnisms for the construction of an entity (including Epigenetics as an alternative controversial mechanism). If you don't understand what mechnisms are involved in construction, talk to Massimo or hire a private tutor.

Read the posts again slowly if you have already read them, or read them for the first time if you haven't. that's my best advice. If you find it hard to understand that the mechanisms are nothing until selected by the environment every moment in the life of an entity, then you have not understood the meaning of causation in adapatation. The environment is the only cause. What I have stated is quite clear, and it's not motor sports, so save your driving for the road, and do some reading. This has been a waste of my time, but a good example of dealing with such replies, for others to read.

Okay. Let me see if I am understanding you correctly: You don't have a problem with Jablonka's and Lamb's proposal of "epigenetic inheritance." But you do have a problem with them characterizing it as the "inheritance of acquired characteristics" or "Lamarckian." Right? Or, am I misunderstanding you?

> They are correct in the second challenge, wrong in the first one. <

Okay. Just to recapitulate: You are stating here that Jablonka and Lamb are wrong to challenge that "all variations in the hereditary material are random" (one of the central tenets of neo-Darwinism).

Questions:

- Is "epigenetic inheritance" random or non-random (adaptive)?

- If we had compelling evidence (this is hypothetical) that "SOME variations in the heriditary material are NONRANDOM (or adaptive)," would that constitute a potential revolution or paradigm shift in evolutionary thought?

> Well, first of all there is a difference of emphasis. But what I (and Coyne) object to is the use of the word "crisis." <

Okay. But Coyne seems to object to your call for an "extended synthesis," characterizing it (or mischaracterizing it) as a call for a "revolution" in evolution theory. So, it would appear that I am not the only one who has misinterpeted what you are calling for; Coyne has too.

"But I [Jerry Coyne] am irritated by the constant appearance of what I call “BIS”–the Big Idea Syndrome. An evolutionist finds a new phenomenon, say transposable elements, or epigenetics, or “modularity,” and suddenly that one phenomenon becomes the centerpiece of a claim that modern evolutionary theory is ripe for a revolution."

> I said it several times, including just above: epigenetic inheritance is real, but there is no ground to call it Lamarckian. <

But what about the other "two dimensions of the four dimensions of evolution" that Jablonka and Lamb have proposed, namely the "behavioral variations" and "symbolic variations" (at first blush, these seem to be somewhat similar to Dawkin's "memetics")? Are you endorsing these two dimensions?

I feel like this discussion is approaching a diminishing return, and a new post is about to come out, so it's likely time to move on. A few additional comments on Alastair's latest:

> You don't have a problem with Jablonka's and Lamb's proposal of "epigenetic inheritance." But you do have a problem with them characterizing it as the "inheritance of acquired characteristics" or "Lamarckian." Right? <

Correct.

> You are stating here that Jablonka and Lamb are wrong to challenge that "all variations in the hereditary material are random" <

Correct again, I don't think there is sufficient evidence for that claim.

> Is "epigenetic inheritance" random or non-random (adaptive)? <

Non-random is not the same as adaptive. Just like mutations, epi-mutations are random and *then* are selected. In other words, the origination (pre-selection) mechanism is random.

> If we had compelling evidence (this is hypothetical) that "SOME variations in the heriditary material are NONRANDOM (or adaptive)," would that constitute a potential revolution or paradigm shift in evolutionary thought? <

Well, it would be a big deal, but it still wouldn't deny several other tenets of Darwinism, particularly the crucial role of natural selection.

> it would appear that I am not the only one who has misinterpeted what you are calling for; Coyne has too. <

Well, you are in good company, but Coyne is wrong nonetheless.

> the "behavioral variations" and "symbolic variations" (at first blush, these seem to be somewhat similar to Dawkin's "memetics")? Are you endorsing these two dimensions? <

No, memetics is a different thing. Yes, I "endorse" them, but so do a number of other biologists. The only (somewhat) controversial one is epigenetic inheritance.